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idonaldson library [108 articles]

Статьи, недавно добавленные в библиотеку idonaldson library ordered by importance.
  • A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--A case study using E2F1.
    Genome Res (19 October 2006)
    by Victor X X Jin, Alina Rabinovich, Sharon L L Squazzo, Roland Green, Peggy J J Farnham
    posted to chip-on-chip crm tfbs tool by idonaldson on 2007-11-08 08:50:56 as ***** along with 2 people aprasad jfr
  • Discovering motifs with transcription factor domain knowledge.
    Pac Symp Biocomput (2007), pp. 472-483.
    by HC Leung, FY Chin, BM Chan
    posted to motif-discovery tfbs tool by idonaldson on 2007-11-12 08:50:57 as **** along with 1 person maximilianh
  • Mining Biological Networks for Unknown Pathways.
    Bioinformatics (30 August 2007)
    by Ali Cakmak, Gultekin Ozsoyoglu
    posted to go networks by idonaldson on 2007-11-06 09:38:08 as **** along with 7 people mdstobbe jyuh tmmurali bluto shigepong cabbagezs acakmak
  • MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs
    BMC Bioinformatics, Vol. 8 (22 March 2007), 100.
    by Mamoru Kato, Tatsuhiko Tsunoda
    posted to cis-regulation crm tool by idonaldson on 2007-11-06 09:15:33 as **** along with 3 people and 1 group isimpson cwbrown nklee EisenLab
  • Regulatory motif discovery using a population clustering evolutionary algorithm.
    IEEE/ACM Trans Comput Biol Bioinform, Vol. 4, No. 3. (p 2007), pp. 403-414.
    by MA Lones, AM Tyrrell
    posted to motif-discovery tool by idonaldson on 2007-10-22 09:26:24 as **** along with 4 people isimpson nklee xili03 csdhwang
  • Discriminative motif discovery in DNA and protein sequences using the DEME Algorithm
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Emma Redhead, Timothy Bailey
    posted to motif-discovery tool by idonaldson on 2007-10-22 09:25:28 as **** along with 5 people and 1 group dpollard cjeans nklee niallhaslam maximilianh EisenLab
  • DBTSS: database of transcription start sites, progress report 2008
    Nucl. Acids Res. (16 October 2007), gkm901.
    by Hiroyuki Wakaguri, Riu Yamashita, Yutaka Suzuki, Sumio Sugano, Kenta Nakai
    posted to promoter tool tss by idonaldson on 2007-10-22 09:22:09 as **** along with 1 person jyuh
  • ChIPping away at gene regulation.
    EMBO reports, Vol. 9, No. 4. (April 2008), pp. 337-343.
    by CE Massie, IG Mills
    posted to review chip-on-chip chip-chip by idonaldson on 2008-07-08 10:53:50 as ***
  • A survey of motif discovery methods in an integrated framework
    Biology Direct, Vol. 1, No. 1. (06 April 2006), 11.
    by Geir K Sandve, Finn Drabløs
    posted to tools review motif-discovery by idonaldson on 2008-07-08 09:03:38 as *** along with 5 people and 1 group aprasad dpollard samal yevishere csdhwang EisenLab
  • Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells
    Genome Res. (15 May 2008), gr.072769.107.
    by Dan Xie, Jun Cai, Na-Yu Chia, Huck Ng, Sheng Zhong
    posted to tool motif-discovery crm cis-regulation by idonaldson on 2008-05-27 09:53:11 as *** along with 4 people phoenixzxl isimpson GustavoLacerda ihpark
  • ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species
    Nucl. Acids Res. (3 May 2008), gkn195.
    by Bart Hooghe, Paco Hulpiau, Frans van Roy, Pieter De Bleser
    posted to transcription-factor tool promoter conserved by idonaldson on 2008-05-13 10:38:49 as *** along with 3 people jyuh maralena maximilianh
  • The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site
    Nucl. Acids Res. (26 March 2008), gkn137.
    by Kannan Tharakaraman, Olivier Bodenreider, David Landsman, John L Spouge, Leonardo Marino-Ramirez
    posted to tss motif by idonaldson on 2008-05-07 10:10:13 as *** along with 2 people fpattyn maximilianh
  • Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets.
    Genome research (14 April 2008)
    by Chaim Linhart, Yonit Halperin, Ron Shamir
    posted to motif-discovery tfbs tool by idonaldson on 2008-04-22 09:26:03 as *** along with 6 people and 1 group tmmurali isimpson fpattyn maximilianh ealloza maralena BergmanLab
  • Transposable elements and the evolution of regulatory networks.
    Nat Rev Genet (27 March 2008)
    by Cédric Feschotte
    posted to networks regulation review te by idonaldson on 2008-04-21 10:24:26 as *** along with 8 people and 1 group pradiptaray smbe2008 eskay roys cmzmasek jonsta247 djkt bootsy BergmanLab
  • Chromhome: A rich internet application for accessing comparative chromosome homology maps
    BMC Bioinformatics, Vol. 9 (26 March 2008), 168.
    by Sridevi Nagarajan, Willem Rens, James Stalker, Tony Cox, Malcolm A Ferguson-Smith
    posted to chromosome comparison tool by idonaldson on 2008-03-31 09:50:58 as *** along with 1 person jyuh
  • Motif discovery in tissue-specific regulatory sequences using directed information.
    EURASIP J Bioinform Syst Biol (2007)
    by A Rao, AO Hero Iii, DJ States, JD Engel
    posted to motif-discovery tissue-specific by idonaldson on 2008-03-17 11:03:58 as *** along with 2 people isimpson maximilianh
  • Assessment of composite motif discovery methods
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Kjetil Klepper, Geir Sandve, Osman Abul, Jostein Johansen, Finn Drablos
    posted to analysis motif-discovery tool by idonaldson on 2008-03-03 09:19:03 as *** along with 6 people and 1 group isimpson chad_davis nklee maximilianh xili03 csdhwang Motif Discovery
  • fdrMotif: Identifying cis-elements by an EM Algorithm Coupled with False Discovery Rate Control.
    Bioinformatics (22 February 2008)
    by Leping Li, Robert L L Bass, Yu Liang
    posted to motif-discovery tool by idonaldson on 2008-02-28 16:05:34 as *** along with 3 people isimpson maximilianh csdhwang
  • Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes
    Genome Biology, Vol. 9 (15 February 2008), R34.
    by Par G Engstrom, David Fredman, Boris Lenhard
    posted to cis-regulation conserved tool by idonaldson on 2008-02-25 10:25:05 as *** along with 5 people isimpson boudinot brant natstreet heliopais
  • Systematic functional characterization of cis-regulatory motifs in human core promoters
    Genome Res. (6 February 2008), gr.6828808.
    by Saurabh Sinha, Adam S Adler, Yair Field, Howard Y Chang, Eran Segal
    posted to cis-regulation motif promoter by idonaldson on 2008-02-20 08:58:19 as *** along with 7 people isimpson ihpark gracio ealloza lp2 cabbagezs emptyhb
  • Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors
    BMC Bioinformatics, Vol. 8 (09 November 2007), 437.
    by Xueping Yu, Jimmy Lin, Donald J Zack, Jiang Qian
    posted to crm tfbs tissue-specific by idonaldson on 2008-02-15 09:28:41 as *** along with 7 people bootsy jyuh chad_davis mikaelhuss nklee maximilianh njcitulike
  • Text-mining assisted regulatory annotation
    Genome Biology, Vol. 9, No. 2. (2008)
    by Stein Aerts, Maximilian Haeussler, Steven van Vooren, Obi Griffith, Paco Hulpiau, Steven Jones, Stephen Montgomery, Casey Bergman, The
    posted to annotation regulation text-mining by idonaldson on 2008-02-14 12:58:31 as *** along with 7 people jyuh bpcusack isimpson dullhunk maximilianh mircea jsjoly
  • Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
    Genome Res. (7 February 2008), gr.7080508.
    by David S Johnson, Wei Li, Benjamin D Gordon, Arindam Bhattacharjee, Bo Curry, Jayati Ghosh, Leonardo Brizuela, Jason S Carroll, Myles Brown, Paul Flicek, Christopher M Koch, Ian Dunham, Mark Bieda, Xiaoqin Xu, Peggy J Farnham, Philipp Kapranov, David A Nix, Thomas R Gingeras, Xinmin Zhang, Heather Holster, Nan Jiang, Roland Green, Jun S Song, Scott A Mccuine, Elizabeth Anton, Loan Nguyen, Nathan D Trinklein, Zhen Ye, Keith Ching, David Hawkins, Bing Ren, Peter C Scacheri, Joel Rozowsky, Alexander Karpikov, Ghia Euskirchen, Sherman Weissman, Mark Gerstein, Michael Snyder, Annie Yang, Zarmik Moqtaderi, Heather Hirsch, Hennady P Shulha, Yutao Fu, Zhiping Weng, Kevin Struhl, Richard M Myers, Jason D Lieb, Shirley X Liu
    posted to chip-on-chip comparison by idonaldson on 2008-02-12 17:07:30 as *** along with 10 people and 2 groups gracio stajich lp2 magusina jfr kengg djkt xiaobeizhao cabbagezs caseybrown Berkeley Mycology BergmanLab
  • CMARRT: a tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure.
    Pac Symp Biocomput (2008), pp. 515-526.
    by PF Kuan, H Chun, S Keleş
    posted to chip-on-chip tool by idonaldson on 2008-02-04 13:14:00 as *** along with 1 person jfr
  • Model-based deconvolution of genome-wide DNA binding.
    Bioinformatics (1 December 2007)
    by David J J Reiss, Marc T T Facciotti, Nitin S S Baliga
    posted to chip-on-chip deconvolution tfbs by idonaldson on 2008-01-31 11:10:21 as *** along with 5 people isimpson vega jyuh djkt yevishere
  • TFBS Identification Based on Genetic Algorithm with Combined Representations and Adaptive Post-processing.
    Bioinformatics (6 December 2007)
    by Tak-Ming M Chan, Kwong-Sak S Leung, Kin-Hong H Lee
    posted to motif-discovery tfbs tool by idonaldson on 2008-01-31 11:07:05 as *** along with 5 people isimpson nklee maximilianh xili03 csdhwang
  • Predicting expression patterns from regulatory sequence in Drosophila segmentation
    Nature (02 January 2008)
    by Eran Segal, Tali Raveh-Sadka, Mark Schroeder, Ulrich Unnerstall, Ulrike Gaul
    posted to expression prediction by idonaldson on 2008-01-31 09:39:38 as *** along with 12 people siebert tresch tmmurali eckart_bindewald djkt bootsy biomcgary roys emptyhb pkharchenko meiklej jrest
  • Functional evolution of the p53 regulatory network through its target response elements
    Proceedings of the National Academy of Sciences (10 January 2008), 0704694105.
    by Anil G Jegga, Alberto Inga, Daniel Menendez, Bruce J Aronow, Michael A Resnick
    posted to evolution networks p53 by idonaldson on 2008-01-14 09:51:08 as *** along with 5 people and 1 group brant cjeans zwang cisevol renatomilani cis-regulatory-evolution
  • Runx genes are direct targets of Scl/Tal1 in the yolk sac and fetal liver.
    Blood (9 January 2008)
    by Josette-Renee R Landry, Sarah Kinston, Kathy Knezevic, Marella F T R F de Bruijn, Nicola Wilson, Wade T T Nottingham, Michael Peitz, Frank Edenhofer, John E E Pimanda, Katrin Ottersbach, Berthold Gottgens
    posted to gottgens by idonaldson on 2008-01-14 09:45:16 as ***
  • A Hybrid Model for Robust Detection of Transcription Factor Binding Sites.
    Bioinformatics (9 January 2008)
    by Sumedha Gunewardena, Zhaolei Zhang
    posted to motif-discovery tfbs tool by idonaldson on 2008-01-14 09:30:49 as *** along with 2 people jyuh maximilianh
  • OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics
    BMC Evolutionary Biology, Vol. 7 (30 November 2007), 241.
    by Vincent Ranwez, Frederic Delsuc, Sylvie Ranwez, Khalid Belkir, Marie-Ka Tilak, Emmanuel JP Douzery
    posted to orthologues phylogenetic tool by idonaldson on 2008-01-10 12:35:15 as *** along with 1 person aprasad
  • Maintenance of transposon-free regions throughout vertebrate evolution
    BMC Genomics, Vol. 8 (20 December 2007), 470.
    by Cas Simons, Igor V Makunin, Michael Pheasant, John S Mattick
    posted to transposon-free-regions by idonaldson on 2008-01-08 09:59:53 as *** along with 2 people and 2 groups blobbybirdman cisevol cis-regulatory-evolution BergmanLab
  • Generic eukaryotic core promoter prediction using structural features of DNA
    Genome Res. (20 December 2007), gr.6991408.
    by Thomas Abeel, Yvan Saeys, Eric Bonnet, Pierre Rouze, Yves Van de Peer
    posted to prediction promoter structural by idonaldson on 2007-12-21 10:22:56 as *** along with 3 people cjeans cabbagezs maximilianh
  • Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting
    Bioinformatics, Vol. 24, No. 1. (1 January 2008), pp. 18-25.
    by Kai Ye, Anton, Jaap Heringa, Adriaan P Ijzerman, Elena Marchiori
    posted to alignment multiple tool by idonaldson on 2007-12-20 12:28:20 as *** along with 1 person h-chi
  • A code for transcription initiation in mammalian genomes
    Genome Res. (21 November 2007), gr.6831208.
    by Martin C Frith, Eivind Valen, Anders Krogh, Yoshihide Hayashizaki, Piero Carninci, Albin Sandelin
    posted to prediction tss by idonaldson on 2007-11-28 08:48:13 as *** along with 7 people dchughes cabbagezs maximilianh oelemento gjuggler ohara gracio
  • OSCAR: One-class SVM for Accurate Recognition of Cis-elements
    Bioinformatics (5 October 2007), btm473.
    by Bo Jiang, Michael Q Zhang, Xuegong Zhang
    posted to cis-regulation tfbs tool by idonaldson on 2007-11-27 14:42:52 as *** along with 6 people and 1 group isimpson cassj tmmurali chad_davis cabbagezs maximilianh csb_journal_club_public
  • Ab initio prediction of transcription factor binding sites.
    Pac Symp Biocomput (2007), pp. 484-495.
    by LA Liu, JS Bader
    posted to prediction tfbs by idonaldson on 2007-11-12 09:14:45 as *** along with 1 person aalibes
  • A systems biology approach for pathway level analysis
    Genome Res. (4 September 2007), gr.6202607.
    by Sorin Draghici, Purvesh Khatri, Adi L Tarca, Kashyap Amin, Arina Done, Calin Voichita, Constantin Georgescu, Roberto Romero
    posted to networks tool by idonaldson on 2007-11-01 08:47:00 as *** along with 15 people and 3 groups AlexanderPico heliopais tmmurali dragonrez jfr gurkanbebek grahamc shigepong zwang cabbagezs cerami xingxu shikin Pao-Yang thomaskelder Bioinformatics ParkinsonLab_at_MaRS OPIG
  • Discovering Motifs in Ranked Lists of DNA Sequences
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e39.
    by Eran Eden, Doron Lipson, Sivan Yogev, Zohar Yakhini
    posted to motif-discovery tool by idonaldson on 2007-10-29 10:38:59 as *** along with 6 people isimpson eckart_bindewald zwang GeeSharpMinor ppark hpaces
  • Gata2, Fli1, and Scl form a recursively wired gene-regulatory circuit during early hematopoietic development.
    Proc Natl Acad Sci U S A (25 October 2007)
    by John E E Pimanda, Katrin Ottersbach, Kathy Knezevic, Sarah Kinston, Wan Y I Y Chan, Nicola K K Wilson, Josette-Renée R Landry, Andrew D D Wood, Anja Kolb-Kokocinski, Anthony R R Green, David Tannahill, Georges Lacaud, Valerie Kouskoff, Berthold Göttgens
    posted to cis-regulation crm gottgens haematopoiesis networks tfbs by idonaldson on 2007-10-29 10:30:29 as *** along with 2 people jjray maximilianh
  • Transposable element fragments in protein-coding regions and their contributions to human functional proteins
    Gene, Vol. 401, No. 1-2. (15 October 2007), pp. 165-171.
    by Ming Wu, Li Li, Zhirong Sun
    posted to human protein-coding te by idonaldson on 2007-10-29 10:19:26 as *** along with 4 people and 3 groups cisevol dchughes N0131826 paulcartwright G4ID Genetics-of-Gambling BergmanLab
  • IEM: An Algorithm for Iterative Enhancement of Motifs Using Comparative Genomics Data.
    Comput Syst Bioinformatics Conf, Vol. 6 (2007), pp. 227-235.
    by E Zeng, K Mathee, G Narasimhan
    posted to cis-regulation conserved tfbs tool by idonaldson on 2007-10-29 10:04:48 as *** along with 3 people isimpson maximilianh annacarina07
  • How does DNA sequence motif discovery work?
    Nature Biotechnology, Vol. 24, No. 8., pp. 959-961.
    by Patrik D'Haeseleer
    posted to cis-regulation motif-discovery primer tfbs by idonaldson on 2007-10-26 14:26:18 as *** along with 4 people and 1 group isimpson okarsligil antonkratz xi03 Bioinformatics
  • The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells
    Nature Genetics, Vol. 38, No. 4. (05 March 2006), pp. 431-440.
    by Yuin-Han Loh, Qiang Wu, Joon-Lin Chew, Vinsensius B Vega, Weiwei Zhang, Xi Chen, Guillaume Bourque, Joshy George, Bernard Leong, Jun Liu, Kee-Yew Wong, Ken W Sung, Charlie WH Lee, Xiao-Dong Zhao, Kuo-Ping Chiu, Leonard Lipovich, Vladimir A Kuznetsov, Paul Robson, Lawrence W Stanton, Chia-Lin Wei, Yijun Ruan, Bing Lim, Huck-Hui Ng
    posted to tfbs cis-regulation mouse networks stem-cells by idonaldson on 2007-10-24 10:11:38 as *** along with 9 people MllePapillon jyuh cmmorel gpalidwor brixtonmc vega eukfn mikaelhuss tdmckee
  • Benchmarking tools for the alignment of functional noncoding DNA.
    BMC Bioinformatics, Vol. 5 (21 January 2004)
    by DA Pollard, CM Bergman, J Stoye, SE Celniker, MB Eisen
    posted to alignment tool by idonaldson on 2007-10-23 15:58:35 as *** along with 4 people and 1 group indigoviolet lilou adijr gjuggler EisenLab
  • MyoD uses overlapping but distinct elements to bind E-box and tetraplex structures of regulatory sequences of muscle-specific genes.
    Nucleic Acids Res (16 October 2007)
    by Jeny Shklover, Shulamit Etzioni, Pnina Weisman-Shomer, Anat Yafe, Eyal Bengal, Michael Fry
    posted to cis-regulation ebox muscle myod tfbs by idonaldson on 2007-10-22 09:23:27 as *** along with 1 person and 1 group jmrivort G-quadruplex
  • OrthoDB: the hierarchical catalog of eukaryotic orthologs.
    Nucleic Acids Res (18 October 2007)
    by Evgenia V V Kriventseva, Nazim Rahman, Octavio Espinosa, Evgeny M M Zdobnov
    posted to orthologues tool by idonaldson on 2007-10-22 09:21:23 as *** along with 1 person jyuh
  • Statistical power of phylo-HMM for evolutionarily conserved element detection
    BMC Bioinformatics, Vol. 8 (05 October 2007), 374.
    by Xiaodan Fan, Jun Zhu, Eric E Schadt, Jun S Liu
    posted to cis-regulation conserved hmm by idonaldson on 2007-10-19 13:13:19 as *** along with 2 people and 1 group isimpson pradiptaray BergmanLab
  • An introduction to ROC analysis
    Pattern Recognition Letters, Vol. 27, No. 8. (June 2006), pp. 861-874.
    by Tom Fawcett
    posted to primer roc by idonaldson on 2007-10-19 12:50:24 as *** along with 21 people and 6 groups jyuh isimpson AbnerCYH ldietz vavi dquest sdvillal xiaoyan2006 dwf camu schlauchi vmoa drivard nklee imrchen kmdaily gsiwo tgyork napvasconcelos cdeane haiyeong Bioinformatics Crypto VT_DLRL Randomness LIVIA BergmanLab
  • DiRE: identifying distant regulatory elements of co-expressed genes
    Nucl. Acids Res., Vol. 36, No. suppl_2. (1 July 2008), pp. W133-139.
    by Valer Gotea, Ivan Ovcharenko
    posted to tool crm by idonaldson on 2008-07-08 09:08:50 as ** along with 1 person Borelli
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